Multiple sequence alignment - TraesCS2B01G408700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G408700 chr2B 100.000 5291 0 0 1 5291 581599909 581594619 0.000000e+00 9771.0
1 TraesCS2B01G408700 chr2D 92.695 5188 253 50 170 5291 493203774 493198647 0.000000e+00 7365.0
2 TraesCS2B01G408700 chr2D 88.889 180 13 4 1 174 493468868 493468690 1.150000e-51 215.0
3 TraesCS2B01G408700 chr2A 92.472 2391 142 24 2533 4905 640221817 640224187 0.000000e+00 3384.0
4 TraesCS2B01G408700 chr2A 90.185 2221 147 28 18 2225 640219236 640221398 0.000000e+00 2828.0
5 TraesCS2B01G408700 chr2A 91.603 393 17 5 4899 5291 640224217 640224593 3.630000e-146 529.0
6 TraesCS2B01G408700 chr2A 85.714 189 20 5 2234 2416 640221575 640221762 5.410000e-45 193.0
7 TraesCS2B01G408700 chr2A 80.000 140 18 6 4 134 81014623 81014761 1.570000e-15 95.3
8 TraesCS2B01G408700 chr7D 85.870 460 50 8 2345 2796 635515208 635515660 4.790000e-130 475.0
9 TraesCS2B01G408700 chr7D 78.718 390 71 11 282 666 493935723 493935341 3.160000e-62 250.0
10 TraesCS2B01G408700 chr7B 85.210 453 57 8 2342 2791 613225531 613225086 1.740000e-124 457.0
11 TraesCS2B01G408700 chr3D 81.585 429 65 3 247 667 90765680 90765258 5.070000e-90 342.0
12 TraesCS2B01G408700 chr3B 80.471 425 67 6 252 667 140236245 140235828 1.430000e-80 311.0
13 TraesCS2B01G408700 chr5B 86.026 229 23 6 2345 2571 634083514 634083735 2.460000e-58 237.0
14 TraesCS2B01G408700 chr6D 78.889 270 53 3 2963 3230 315363881 315363614 4.210000e-41 180.0
15 TraesCS2B01G408700 chr3A 79.051 253 38 3 430 667 107023930 107023678 5.480000e-35 159.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G408700 chr2B 581594619 581599909 5290 True 9771.0 9771 100.0000 1 5291 1 chr2B.!!$R1 5290
1 TraesCS2B01G408700 chr2D 493198647 493203774 5127 True 7365.0 7365 92.6950 170 5291 1 chr2D.!!$R1 5121
2 TraesCS2B01G408700 chr2A 640219236 640224593 5357 False 1733.5 3384 89.9935 18 5291 4 chr2A.!!$F2 5273

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
153 156 0.944386 CAAGATTTACCCATCCGCGG 59.056 55.0 22.12 22.12 0.00 6.46 F
1860 1884 0.043310 GCGTGAACGAACTGTGACAC 60.043 55.0 7.10 0.00 43.02 3.67 F
2144 2172 0.459489 GCTCTTGGTTTGTTGGTGCA 59.541 50.0 0.00 0.00 0.00 4.57 F
2995 3260 0.323178 AATGGCTGGCTGAGGTTCAG 60.323 55.0 2.00 1.75 46.90 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 1943 0.101040 CTTCTCTCTCCTGCGAGCTG 59.899 60.0 0.00 0.0 35.94 4.24 R
2992 3257 0.389817 CCACGATGCCGAGAAACTGA 60.390 55.0 0.00 0.0 39.50 3.41 R
4109 4402 0.401356 TGGTGCCTCATGAAGAAGCA 59.599 50.0 0.00 0.0 41.27 3.91 R
4703 5011 1.028868 CCTGGCCTTTACAGCTCAGC 61.029 60.0 3.32 0.0 34.65 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.720046 ACCGTGATCTATGCTTCTCTCTA 58.280 43.478 0.00 0.00 0.00 2.43
59 60 1.646189 CTTCTCTCTAAAGCCGCCAC 58.354 55.000 0.00 0.00 0.00 5.01
71 72 2.267961 CGCCACCACTACCCCTTC 59.732 66.667 0.00 0.00 0.00 3.46
73 74 2.987125 CCACCACTACCCCTTCCG 59.013 66.667 0.00 0.00 0.00 4.30
89 90 3.697747 CGGGTTCCGGTGCTACCA 61.698 66.667 0.00 0.00 44.15 3.25
90 91 2.046604 GGGTTCCGGTGCTACCAC 60.047 66.667 0.00 0.00 38.47 4.16
110 111 3.655211 CTGCTCCCCAGCCCAGTT 61.655 66.667 0.00 0.00 46.26 3.16
111 112 3.635268 CTGCTCCCCAGCCCAGTTC 62.635 68.421 0.00 0.00 46.26 3.01
112 113 4.432741 GCTCCCCAGCCCAGTTCC 62.433 72.222 0.00 0.00 40.14 3.62
113 114 3.732849 CTCCCCAGCCCAGTTCCC 61.733 72.222 0.00 0.00 0.00 3.97
116 117 4.052518 CCCAGCCCAGTTCCCCAG 62.053 72.222 0.00 0.00 0.00 4.45
117 118 4.748144 CCAGCCCAGTTCCCCAGC 62.748 72.222 0.00 0.00 0.00 4.85
118 119 4.748144 CAGCCCAGTTCCCCAGCC 62.748 72.222 0.00 0.00 0.00 4.85
137 138 2.883386 GCCATCCTTAATCTCCAGCAAG 59.117 50.000 0.00 0.00 0.00 4.01
153 156 0.944386 CAAGATTTACCCATCCGCGG 59.056 55.000 22.12 22.12 0.00 6.46
174 177 2.742116 GCCGCCACTATCCCTTCCA 61.742 63.158 0.00 0.00 0.00 3.53
175 178 1.447643 CCGCCACTATCCCTTCCAG 59.552 63.158 0.00 0.00 0.00 3.86
237 240 1.549950 GCCAACCCTGAATCTTTCCCA 60.550 52.381 0.00 0.00 0.00 4.37
304 307 9.220767 AGTAATTCTTTTTCAGTAGTGGCTAAG 57.779 33.333 0.00 0.00 0.00 2.18
347 350 5.083533 ACTCCTGCTAGCATAATAGATGC 57.916 43.478 19.72 1.21 44.85 3.91
366 369 7.565323 AGATGCCATTAAGTTTCTTCTCATC 57.435 36.000 0.00 0.00 0.00 2.92
382 385 3.840666 TCTCATCCAGCTGTCCTAAAACT 59.159 43.478 13.81 0.00 0.00 2.66
420 423 2.279921 CACGAGCGTCACACATTATCTG 59.720 50.000 0.00 0.00 0.00 2.90
448 451 3.199442 TCATCCCACTTAGGAGGTTGA 57.801 47.619 0.00 1.13 39.95 3.18
463 466 2.844348 AGGTTGAATGATCGGGGTAGTT 59.156 45.455 0.00 0.00 0.00 2.24
490 493 4.983053 AGGCATCCCTCAGATTTTCATAG 58.017 43.478 0.00 0.00 36.46 2.23
500 503 7.941238 CCCTCAGATTTTCATAGGTCAATACAT 59.059 37.037 0.00 0.00 0.00 2.29
601 604 4.101430 CCTATAAAAACTTGCATGCCCCAT 59.899 41.667 16.68 0.00 0.00 4.00
781 785 6.461110 TCTAGATTACCAAACGACCTAAGG 57.539 41.667 0.00 0.00 0.00 2.69
879 883 5.735922 GCAAGATAGCAAAACACCAGTCAAA 60.736 40.000 0.00 0.00 0.00 2.69
892 896 4.987912 CACCAGTCAAAAACAACACAACTT 59.012 37.500 0.00 0.00 0.00 2.66
921 925 4.279922 TGACTCCAAAGATGACAACGACTA 59.720 41.667 0.00 0.00 0.00 2.59
930 934 4.449068 AGATGACAACGACTAAAGCACAAG 59.551 41.667 0.00 0.00 0.00 3.16
967 971 2.042831 GCCACCAGCCATGAGTCAC 61.043 63.158 0.00 0.00 34.35 3.67
994 998 3.918591 ACTCGCACAAGTGTAAATAGTCG 59.081 43.478 1.79 0.00 0.00 4.18
1014 1018 0.110823 GCACGATGTCACCGAACAAC 60.111 55.000 0.00 0.00 31.81 3.32
1018 1022 1.068474 GATGTCACCGAACAACGAGG 58.932 55.000 0.00 0.00 45.77 4.63
1070 1074 0.961753 CAGGCCACAAAAGGAGAACC 59.038 55.000 5.01 0.00 0.00 3.62
1095 1099 1.000955 AGTGGACGAGCACAAACTAGG 59.999 52.381 0.00 0.00 0.00 3.02
1121 1128 1.359848 GGGCATGAGTCGTACAACAG 58.640 55.000 0.00 0.00 0.00 3.16
1163 1170 2.420466 AAACAAACGAGGGGCGGGAT 62.420 55.000 0.00 0.00 46.49 3.85
1174 1181 2.340443 GCGGGATAGCGAAGGAGG 59.660 66.667 0.00 0.00 0.00 4.30
1175 1182 2.340443 CGGGATAGCGAAGGAGGC 59.660 66.667 0.00 0.00 0.00 4.70
1206 1213 2.824041 CCCCAAAGCCATCCGACG 60.824 66.667 0.00 0.00 0.00 5.12
1285 1292 6.180472 ACCTATGAATCGAAACTTTCCACAT 58.820 36.000 0.00 0.00 0.00 3.21
1291 1298 3.145286 TCGAAACTTTCCACATGCATCA 58.855 40.909 0.00 0.00 0.00 3.07
1303 1310 2.713167 ACATGCATCAAGGCCCTATAGT 59.287 45.455 0.00 0.00 0.00 2.12
1317 1324 4.799917 GCCCTATAGTCGGGACAAGATTTC 60.800 50.000 0.00 0.00 44.90 2.17
1332 1339 3.607741 AGATTTCAGCATCACACTGGAG 58.392 45.455 0.00 0.00 35.78 3.86
1365 1372 1.760875 GATGTCCGGTCCCTAGCCA 60.761 63.158 0.00 0.00 0.00 4.75
1387 1394 1.068885 AGCAGTCAAGAACGACGAGAG 60.069 52.381 0.00 0.00 40.98 3.20
1450 1458 5.104259 AGATGAAATTCCTAGCGAGGTTT 57.896 39.130 13.04 6.95 44.19 3.27
1479 1490 4.542697 TGTTTCCTTTTTGCTTAGACCCT 58.457 39.130 0.00 0.00 0.00 4.34
1494 1505 0.753262 ACCCTAGTAGCAATGCTCCG 59.247 55.000 12.53 0.00 40.44 4.63
1514 1525 0.247894 GCAACATAAATCGCCGCGAA 60.248 50.000 21.02 3.46 39.99 4.70
1656 1668 2.156343 AACCTCTGTTGAACTCGAGC 57.844 50.000 13.61 0.00 32.13 5.03
1741 1753 2.491271 GCAAATTCAGCGCGCGAAG 61.491 57.895 37.18 24.60 0.00 3.79
1800 1824 5.428253 GTCAAGGTGCAGAAGGATAACATA 58.572 41.667 0.00 0.00 0.00 2.29
1801 1825 5.525378 GTCAAGGTGCAGAAGGATAACATAG 59.475 44.000 0.00 0.00 0.00 2.23
1802 1826 5.189736 TCAAGGTGCAGAAGGATAACATAGT 59.810 40.000 0.00 0.00 0.00 2.12
1803 1827 5.028549 AGGTGCAGAAGGATAACATAGTG 57.971 43.478 0.00 0.00 0.00 2.74
1804 1828 4.130118 GGTGCAGAAGGATAACATAGTGG 58.870 47.826 0.00 0.00 0.00 4.00
1805 1829 4.384208 GGTGCAGAAGGATAACATAGTGGT 60.384 45.833 0.00 0.00 0.00 4.16
1806 1830 4.811557 GTGCAGAAGGATAACATAGTGGTC 59.188 45.833 0.00 0.00 0.00 4.02
1807 1831 4.469586 TGCAGAAGGATAACATAGTGGTCA 59.530 41.667 0.00 0.00 0.00 4.02
1808 1832 5.045942 TGCAGAAGGATAACATAGTGGTCAA 60.046 40.000 0.00 0.00 0.00 3.18
1809 1833 5.294552 GCAGAAGGATAACATAGTGGTCAAC 59.705 44.000 0.00 0.00 0.00 3.18
1810 1834 6.406370 CAGAAGGATAACATAGTGGTCAACA 58.594 40.000 0.00 0.00 0.00 3.33
1811 1835 7.050377 CAGAAGGATAACATAGTGGTCAACAT 58.950 38.462 0.00 0.00 0.00 2.71
1822 1846 2.622942 GTGGTCAACATTTCTTGGCAGA 59.377 45.455 0.00 0.00 0.00 4.26
1833 1857 0.535102 CTTGGCAGACGGGACAAGTT 60.535 55.000 10.41 0.00 46.61 2.66
1834 1858 0.817634 TTGGCAGACGGGACAAGTTG 60.818 55.000 0.00 0.00 30.72 3.16
1835 1859 2.617274 GGCAGACGGGACAAGTTGC 61.617 63.158 1.81 0.00 0.00 4.17
1836 1860 1.891919 GCAGACGGGACAAGTTGCA 60.892 57.895 1.81 0.00 0.00 4.08
1857 1881 1.142097 TGGCGTGAACGAACTGTGA 59.858 52.632 7.10 0.00 43.02 3.58
1859 1883 1.149361 GGCGTGAACGAACTGTGACA 61.149 55.000 7.10 0.00 43.02 3.58
1860 1884 0.043310 GCGTGAACGAACTGTGACAC 60.043 55.000 7.10 0.00 43.02 3.67
1861 1885 0.575390 CGTGAACGAACTGTGACACC 59.425 55.000 2.45 0.00 43.02 4.16
1862 1886 1.801395 CGTGAACGAACTGTGACACCT 60.801 52.381 2.45 0.00 43.02 4.00
1863 1887 2.277084 GTGAACGAACTGTGACACCTT 58.723 47.619 2.45 0.00 34.64 3.50
1864 1888 3.450578 GTGAACGAACTGTGACACCTTA 58.549 45.455 2.45 0.00 34.64 2.69
1912 1936 2.158254 TGGTACATATCGCTACGCTACG 59.842 50.000 0.00 0.00 0.00 3.51
1913 1937 2.475187 GGTACATATCGCTACGCTACGG 60.475 54.545 0.00 0.00 0.00 4.02
1914 1938 1.516161 ACATATCGCTACGCTACGGA 58.484 50.000 0.00 0.00 0.00 4.69
1915 1939 1.196354 ACATATCGCTACGCTACGGAC 59.804 52.381 0.00 0.00 0.00 4.79
1916 1940 1.463831 CATATCGCTACGCTACGGACT 59.536 52.381 0.00 0.00 0.00 3.85
1917 1941 1.143305 TATCGCTACGCTACGGACTC 58.857 55.000 0.00 0.00 0.00 3.36
1918 1942 1.829349 ATCGCTACGCTACGGACTCG 61.829 60.000 0.00 0.00 43.02 4.18
1919 1943 2.352115 GCTACGCTACGGACTCGC 60.352 66.667 0.00 0.00 40.63 5.03
1920 1944 3.095911 CTACGCTACGGACTCGCA 58.904 61.111 0.00 0.00 40.63 5.10
1921 1945 1.011019 CTACGCTACGGACTCGCAG 60.011 63.158 0.00 0.00 40.63 5.18
1925 1949 2.023461 CTACGGACTCGCAGCTCG 59.977 66.667 0.00 0.00 40.63 5.03
1926 1950 4.175489 TACGGACTCGCAGCTCGC 62.175 66.667 0.00 0.00 40.63 5.03
2034 2058 0.657368 CTTGCAAAACCGCGTGACTC 60.657 55.000 4.92 0.00 33.35 3.36
2036 2060 1.082756 GCAAAACCGCGTGACTCTG 60.083 57.895 4.92 0.00 0.00 3.35
2037 2061 1.772063 GCAAAACCGCGTGACTCTGT 61.772 55.000 4.92 0.00 0.00 3.41
2038 2062 1.493772 CAAAACCGCGTGACTCTGTA 58.506 50.000 4.92 0.00 0.00 2.74
2039 2063 1.455786 CAAAACCGCGTGACTCTGTAG 59.544 52.381 4.92 0.00 0.00 2.74
2040 2064 0.672342 AAACCGCGTGACTCTGTAGT 59.328 50.000 4.92 0.00 39.21 2.73
2132 2160 3.233355 GGTGTGGTACAGCTCTTGG 57.767 57.895 4.08 0.00 42.83 3.61
2144 2172 0.459489 GCTCTTGGTTTGTTGGTGCA 59.541 50.000 0.00 0.00 0.00 4.57
2231 2433 3.415212 TCTTCCATCTGCCAGAAACTTG 58.585 45.455 0.00 0.00 0.00 3.16
2244 2446 3.077359 AGAAACTTGGCTTCTTCATCGG 58.923 45.455 0.00 0.00 28.46 4.18
2249 2451 2.024176 TGGCTTCTTCATCGGTTAGC 57.976 50.000 0.00 0.00 0.00 3.09
2272 2474 2.163613 CCTTCCCCTATGTTGTTTTCGC 59.836 50.000 0.00 0.00 0.00 4.70
2327 2533 8.091385 ACGACAAAACTCCTTATTTTTATCGT 57.909 30.769 7.17 7.17 40.25 3.73
2372 2580 4.040706 TGTGATTCGGGTAGGTTACAAACT 59.959 41.667 0.00 0.00 0.00 2.66
2386 2594 5.448360 GGTTACAAACTACTACGATCGAGCT 60.448 44.000 24.34 1.27 0.00 4.09
2413 2650 1.844687 GCCAGCTTCCTCCAAGAAAT 58.155 50.000 0.00 0.00 33.29 2.17
2414 2651 1.475682 GCCAGCTTCCTCCAAGAAATG 59.524 52.381 0.00 0.00 33.29 2.32
2426 2663 2.360165 CCAAGAAATGGGCTGTCTATGC 59.640 50.000 0.00 0.00 46.27 3.14
2427 2664 4.804133 CCAAGAAATGGGCTGTCTATGCC 61.804 52.174 0.00 0.00 46.27 4.40
2434 2671 2.086054 GGCTGTCTATGCCTATTCCG 57.914 55.000 0.00 0.00 46.38 4.30
2435 2672 1.338200 GGCTGTCTATGCCTATTCCGG 60.338 57.143 0.00 0.00 46.38 5.14
2436 2673 1.338200 GCTGTCTATGCCTATTCCGGG 60.338 57.143 0.00 0.00 0.00 5.73
2437 2674 2.248248 CTGTCTATGCCTATTCCGGGA 58.752 52.381 0.00 0.00 0.00 5.14
2438 2675 1.968493 TGTCTATGCCTATTCCGGGAC 59.032 52.381 0.00 0.00 0.00 4.46
2439 2676 1.968493 GTCTATGCCTATTCCGGGACA 59.032 52.381 0.00 0.00 0.00 4.02
2440 2677 2.367567 GTCTATGCCTATTCCGGGACAA 59.632 50.000 0.00 0.00 0.00 3.18
2441 2678 3.042682 TCTATGCCTATTCCGGGACAAA 58.957 45.455 0.00 0.00 0.00 2.83
2466 2703 3.760035 GCAAGAGACGGCCGGAGA 61.760 66.667 31.76 0.00 0.00 3.71
2467 2704 2.970639 CAAGAGACGGCCGGAGAA 59.029 61.111 31.76 0.00 0.00 2.87
2519 2756 2.493030 GCCTCTTACTACGCCGCA 59.507 61.111 0.00 0.00 0.00 5.69
2525 2762 2.077801 CTTACTACGCCGCATGCACG 62.078 60.000 23.91 23.91 41.33 5.34
2613 2862 4.147449 CATCCGACGGCTCAGGCA 62.147 66.667 9.66 0.00 40.87 4.75
2885 3134 1.214589 GGTACCGACACTGCGATGT 59.785 57.895 0.00 0.00 34.78 3.06
2898 3147 3.873361 ACTGCGATGTAATTCCATCACTG 59.127 43.478 11.12 7.80 41.06 3.66
2922 3171 3.325135 AGAATTCAAGTGTCTCCGGAGTT 59.675 43.478 30.17 15.01 0.00 3.01
2924 3173 4.884668 ATTCAAGTGTCTCCGGAGTTTA 57.115 40.909 30.17 15.17 0.00 2.01
2947 3212 3.176411 ACTCCAACACCTGATCTGATCA 58.824 45.455 18.61 18.61 37.76 2.92
2986 3251 0.610232 GACACAAGGAATGGCTGGCT 60.610 55.000 2.00 0.00 0.00 4.75
2992 3257 1.000396 GGAATGGCTGGCTGAGGTT 60.000 57.895 2.00 0.00 0.00 3.50
2995 3260 0.323178 AATGGCTGGCTGAGGTTCAG 60.323 55.000 2.00 1.75 46.90 3.02
2998 3263 0.538287 GGCTGGCTGAGGTTCAGTTT 60.538 55.000 7.80 0.00 45.94 2.66
3010 3275 1.126846 GTTCAGTTTCTCGGCATCGTG 59.873 52.381 0.00 0.00 37.69 4.35
3148 3413 2.227036 CCCAGAGCACCCTGTCCTT 61.227 63.158 0.00 0.00 32.43 3.36
3208 3473 3.387962 TGAAGGGTTGCTCTATCTCCAT 58.612 45.455 0.00 0.00 0.00 3.41
3345 3618 1.000955 AGGCAGACAGTTTCTACACCG 59.999 52.381 0.00 0.00 31.12 4.94
3386 3659 6.485648 TCATGGCATCAGAACTGAATTATGAG 59.514 38.462 8.59 0.00 41.70 2.90
3388 3661 4.820716 GGCATCAGAACTGAATTATGAGCT 59.179 41.667 8.59 0.00 41.70 4.09
3389 3662 5.994054 GGCATCAGAACTGAATTATGAGCTA 59.006 40.000 8.59 0.00 41.70 3.32
3390 3663 6.147492 GGCATCAGAACTGAATTATGAGCTAG 59.853 42.308 8.59 0.00 41.70 3.42
3395 3668 9.628500 TCAGAACTGAATTATGAGCTAGTACTA 57.372 33.333 1.89 1.89 33.56 1.82
3406 3679 6.852420 TGAGCTAGTACTACATGGAAAAGT 57.148 37.500 0.00 0.00 0.00 2.66
3411 3684 7.178628 AGCTAGTACTACATGGAAAAGTCAGAA 59.821 37.037 0.00 0.00 0.00 3.02
3486 3765 7.951030 CGATATCTGTAGATTATATACCGCGAC 59.049 40.741 8.23 0.00 36.05 5.19
3528 3807 2.303022 GTTGGATGAGGAGTTCAGACCA 59.697 50.000 0.00 0.00 41.32 4.02
3534 3813 3.808728 TGAGGAGTTCAGACCAAAACTG 58.191 45.455 0.00 0.00 35.90 3.16
3543 3822 2.544267 CAGACCAAAACTGTCGGACTTC 59.456 50.000 9.88 0.00 37.80 3.01
3567 3846 2.856208 TAGCAAGGGAGGGGCCATCA 62.856 60.000 21.12 0.00 38.95 3.07
3585 3864 2.862541 TCAGAAGGTCAAACCCATGTG 58.137 47.619 0.00 0.00 39.75 3.21
3605 3885 6.109156 TGTGTCTACAGTGGTATGTCAAAT 57.891 37.500 0.00 0.00 34.56 2.32
3613 3893 9.383519 CTACAGTGGTATGTCAAATTTCACTAT 57.616 33.333 6.22 0.00 34.56 2.12
3691 3973 4.649692 GTTCCATATGGAGCATCTCACAT 58.350 43.478 28.18 0.00 46.36 3.21
3694 3976 5.336102 TCCATATGGAGCATCTCACATAGA 58.664 41.667 20.98 0.00 39.78 1.98
3695 3977 5.421374 TCCATATGGAGCATCTCACATAGAG 59.579 44.000 20.98 0.00 41.74 2.43
3696 3978 5.187381 CCATATGGAGCATCTCACATAGAGT 59.813 44.000 17.49 0.00 40.64 3.24
3697 3979 4.870123 ATGGAGCATCTCACATAGAGTC 57.130 45.455 0.00 0.00 44.98 3.36
3698 3980 2.620585 TGGAGCATCTCACATAGAGTCG 59.379 50.000 0.00 0.00 44.98 4.18
3699 3981 2.606795 GGAGCATCTCACATAGAGTCGC 60.607 54.545 0.00 0.00 44.98 5.19
3700 3982 2.305928 AGCATCTCACATAGAGTCGCT 58.694 47.619 0.00 0.00 44.98 4.93
3759 4052 1.066303 GCTCCAGACTATGTCCAGACG 59.934 57.143 0.00 0.00 32.18 4.18
3822 4115 7.200434 AGTGGTAATGTATGAAATCCTCACT 57.800 36.000 0.00 0.00 36.69 3.41
3942 4235 0.756294 TCGACACAAGGCTTGAAGGA 59.244 50.000 32.50 19.38 0.00 3.36
3945 4238 1.882623 GACACAAGGCTTGAAGGAAGG 59.117 52.381 32.50 14.21 31.56 3.46
3972 4265 3.388676 CCATGAGAGGAGCAAGAGAGATT 59.611 47.826 0.00 0.00 0.00 2.40
4083 4376 2.154462 CACAAGGAACTGGATGGTCAC 58.846 52.381 0.00 0.00 40.86 3.67
4109 4402 1.543429 CCGTTCAGTGGAGGAAAGCTT 60.543 52.381 0.00 0.00 0.00 3.74
4140 4433 2.203153 GCACCAACGACACCACCT 60.203 61.111 0.00 0.00 0.00 4.00
4273 4567 1.975407 CCTCGGACGTGTACCCTGT 60.975 63.158 0.00 0.00 0.00 4.00
4296 4590 3.542712 TCGTTGAGCTCTTGATTTTGC 57.457 42.857 16.19 0.00 0.00 3.68
4326 4620 9.662545 ATTTTGTTTTCTTGTTGTTCTGTTTTG 57.337 25.926 0.00 0.00 0.00 2.44
4380 4680 0.107508 TTCTCCAGTGCCATAGCTGC 60.108 55.000 0.00 0.00 40.80 5.25
4404 4704 7.025963 GCTGATTGATGAGTAAAGTTTGAAGG 58.974 38.462 0.00 0.00 0.00 3.46
4486 4789 5.118990 GCCTCACATGAGCTAGTAATTTGA 58.881 41.667 0.00 0.00 40.75 2.69
4548 4851 3.334691 TCTTTGGAATAGTGGAAGCACG 58.665 45.455 0.00 0.00 0.00 5.34
4561 4864 7.385778 AGTGGAAGCACGCTATTTTATTTTA 57.614 32.000 0.00 0.00 0.00 1.52
4677 4985 2.820787 ACTACAGGAGGAACAGAGAACG 59.179 50.000 0.00 0.00 0.00 3.95
4703 5011 4.711949 AAGCGGGCAGGTCAGCAG 62.712 66.667 0.00 0.00 35.83 4.24
4737 5045 1.679153 GCCAGGACGGTTTTTCTTTGA 59.321 47.619 0.00 0.00 36.97 2.69
4745 5053 6.429078 AGGACGGTTTTTCTTTGATAGGTTAC 59.571 38.462 0.00 0.00 0.00 2.50
4804 5112 1.227383 CCATGCCCCCTTGTACTCC 59.773 63.158 0.00 0.00 0.00 3.85
4808 5116 1.303282 GCCCCCTTGTACTCCCTTG 59.697 63.158 0.00 0.00 0.00 3.61
4850 5158 6.874134 CCCTCAACTGATTACCTATATTTCCG 59.126 42.308 0.00 0.00 0.00 4.30
4893 5201 3.818180 TGCTAAAACCCCAAGAAACGTA 58.182 40.909 0.00 0.00 0.00 3.57
4945 5291 6.150140 AGCTCATGACACAGAAAGTTAAATCC 59.850 38.462 0.00 0.00 0.00 3.01
4977 5323 3.036819 AGCATCAGCATCCTCTTCAGTA 58.963 45.455 0.00 0.00 45.49 2.74
4979 5325 3.391965 CATCAGCATCCTCTTCAGTAGC 58.608 50.000 0.00 0.00 0.00 3.58
5025 5371 3.315191 GTGTGGCATTGTAACAACAGAGT 59.685 43.478 0.00 0.00 0.00 3.24
5032 5378 4.875544 TTGTAACAACAGAGTGAACAGC 57.124 40.909 0.00 0.00 0.00 4.40
5106 5452 9.819267 AATTAAACACCGAAGAATTAAAAACCA 57.181 25.926 0.00 0.00 0.00 3.67
5136 5482 4.067192 CAGGTCATGAGTCATCACACAAA 58.933 43.478 9.52 0.00 38.57 2.83
5188 5534 4.938832 CCAATCTTGTTGTTACCCATACGA 59.061 41.667 0.00 0.00 0.00 3.43
5206 5552 1.317611 CGATAGCACTTGACGTTCACG 59.682 52.381 0.00 0.00 46.33 4.35
5242 5588 2.042230 ACGCGGTTATCCTCCCCT 60.042 61.111 12.47 0.00 0.00 4.79
5284 5630 1.803519 GAGTGCCAGCTCGAACTCG 60.804 63.158 3.46 0.00 41.45 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.033602 GGTAGTGGTGGCGGCTTT 59.966 61.111 11.43 0.00 0.00 3.51
73 74 2.046604 GTGGTAGCACCGGAACCC 60.047 66.667 9.46 0.39 42.58 4.11
93 94 3.635268 GAACTGGGCTGGGGAGCAG 62.635 68.421 0.00 0.00 36.33 4.24
96 97 3.732849 GGGAACTGGGCTGGGGAG 61.733 72.222 0.00 0.00 0.00 4.30
109 110 2.443255 GAGATTAAGGATGGCTGGGGAA 59.557 50.000 0.00 0.00 0.00 3.97
110 111 2.057922 GAGATTAAGGATGGCTGGGGA 58.942 52.381 0.00 0.00 0.00 4.81
111 112 1.074566 GGAGATTAAGGATGGCTGGGG 59.925 57.143 0.00 0.00 0.00 4.96
112 113 1.776667 TGGAGATTAAGGATGGCTGGG 59.223 52.381 0.00 0.00 0.00 4.45
113 114 2.813354 GCTGGAGATTAAGGATGGCTGG 60.813 54.545 0.00 0.00 0.00 4.85
114 115 2.158711 TGCTGGAGATTAAGGATGGCTG 60.159 50.000 0.00 0.00 0.00 4.85
115 116 2.130193 TGCTGGAGATTAAGGATGGCT 58.870 47.619 0.00 0.00 0.00 4.75
116 117 2.645838 TGCTGGAGATTAAGGATGGC 57.354 50.000 0.00 0.00 0.00 4.40
117 118 4.428294 TCTTGCTGGAGATTAAGGATGG 57.572 45.455 0.00 0.00 0.00 3.51
118 119 6.956202 AAATCTTGCTGGAGATTAAGGATG 57.044 37.500 9.79 0.00 43.66 3.51
119 120 7.001073 GGTAAATCTTGCTGGAGATTAAGGAT 58.999 38.462 9.79 0.34 43.66 3.24
137 138 4.058797 CCCGCGGATGGGTAAATC 57.941 61.111 30.73 0.00 44.76 2.17
159 162 4.887615 GCTGGAAGGGATAGTGGC 57.112 61.111 0.00 0.00 0.00 5.01
197 200 3.555324 TGGCTGGTCGAACTGGCA 61.555 61.111 28.67 28.67 41.32 4.92
237 240 5.387113 TGATATGTTTAGATTGGGTGGCT 57.613 39.130 0.00 0.00 0.00 4.75
304 307 5.717119 AGTTTGGATGATGATCAAAAGCAC 58.283 37.500 0.00 0.00 32.97 4.40
347 350 5.884792 AGCTGGATGAGAAGAAACTTAATGG 59.115 40.000 0.00 0.00 0.00 3.16
363 366 2.421424 GCAGTTTTAGGACAGCTGGATG 59.579 50.000 19.93 4.11 0.00 3.51
366 369 2.079925 GAGCAGTTTTAGGACAGCTGG 58.920 52.381 19.93 0.00 41.65 4.85
399 402 2.279921 CAGATAATGTGTGACGCTCGTG 59.720 50.000 0.00 0.00 0.00 4.35
400 403 2.163613 TCAGATAATGTGTGACGCTCGT 59.836 45.455 0.00 0.00 0.00 4.18
402 405 4.033358 CCTTTCAGATAATGTGTGACGCTC 59.967 45.833 0.00 0.00 28.46 5.03
448 451 4.505039 GCCTTGATAACTACCCCGATCATT 60.505 45.833 0.00 0.00 0.00 2.57
463 466 5.103982 TGAAAATCTGAGGGATGCCTTGATA 60.104 40.000 18.18 5.25 34.45 2.15
534 537 8.029618 ACCAAAACCACTCACTAACCTTTTGG 62.030 42.308 14.52 14.52 46.11 3.28
723 727 0.326595 TGGCGATGTATGGGTTGTGT 59.673 50.000 0.00 0.00 0.00 3.72
752 756 5.116882 GTCGTTTGGTAATCTAGATGGCTT 58.883 41.667 5.86 0.00 0.00 4.35
764 768 4.004982 GCAATCCTTAGGTCGTTTGGTAA 58.995 43.478 0.00 0.00 0.00 2.85
765 769 3.602483 GCAATCCTTAGGTCGTTTGGTA 58.398 45.455 0.00 0.00 0.00 3.25
798 802 8.321353 TGAGTTTGTTGACCTATTAGTCATGAT 58.679 33.333 0.00 0.00 45.80 2.45
802 806 7.038302 AGGATGAGTTTGTTGACCTATTAGTCA 60.038 37.037 0.00 0.00 44.89 3.41
813 817 7.232737 TGTTCTAGTCTAGGATGAGTTTGTTGA 59.767 37.037 7.05 0.00 0.00 3.18
879 883 7.033185 GGAGTCATGTTTAAGTTGTGTTGTTT 58.967 34.615 0.00 0.00 0.00 2.83
892 896 6.073276 CGTTGTCATCTTTGGAGTCATGTTTA 60.073 38.462 0.00 0.00 0.00 2.01
921 925 0.465287 CCTTGGGTTGCTTGTGCTTT 59.535 50.000 0.00 0.00 40.48 3.51
930 934 0.740737 CGGATTCATCCTTGGGTTGC 59.259 55.000 4.30 0.00 44.93 4.17
994 998 1.225376 TTGTTCGGTGACATCGTGCC 61.225 55.000 8.18 0.00 0.00 5.01
1029 1033 2.265739 GCTGTCGGTCTGATGGCA 59.734 61.111 0.00 0.00 0.00 4.92
1060 1064 0.977395 CCACTCCTCGGTTCTCCTTT 59.023 55.000 0.00 0.00 0.00 3.11
1070 1074 2.142357 TTGTGCTCGTCCACTCCTCG 62.142 60.000 9.02 0.00 36.68 4.63
1095 1099 3.493303 GACTCATGCCCCTCCCCC 61.493 72.222 0.00 0.00 0.00 5.40
1100 1104 0.249398 GTTGTACGACTCATGCCCCT 59.751 55.000 5.96 0.00 0.00 4.79
1107 1114 0.240145 CCTCGCTGTTGTACGACTCA 59.760 55.000 14.38 0.00 34.08 3.41
1141 1148 1.407162 CCCGCCCCTCGTTTGTTTATA 60.407 52.381 0.00 0.00 36.19 0.98
1182 1189 4.973174 TGGCTTTGGGGCATTTCT 57.027 50.000 0.00 0.00 45.79 2.52
1206 1213 0.108567 GTTCTGCCTCGTCTTCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
1285 1292 1.344438 CGACTATAGGGCCTTGATGCA 59.656 52.381 13.45 0.00 0.00 3.96
1303 1310 2.027285 TGATGCTGAAATCTTGTCCCGA 60.027 45.455 0.00 0.00 0.00 5.14
1317 1324 2.232208 TGTCTACTCCAGTGTGATGCTG 59.768 50.000 0.00 0.00 0.00 4.41
1332 1339 3.243234 CGGACATCTGTCTCCATGTCTAC 60.243 52.174 9.98 0.00 45.63 2.59
1365 1372 2.128035 CTCGTCGTTCTTGACTGCTTT 58.872 47.619 0.00 0.00 36.71 3.51
1387 1394 1.571460 CGCTTCACTGCCAAGTCAC 59.429 57.895 0.00 0.00 32.98 3.67
1473 1484 2.043227 GGAGCATTGCTACTAGGGTCT 58.957 52.381 13.88 0.00 39.88 3.85
1479 1490 2.207580 TGCCGGAGCATTGCTACTA 58.792 52.632 18.52 2.57 46.52 1.82
1494 1505 1.654137 CGCGGCGATTTATGTTGCC 60.654 57.895 19.16 0.00 43.93 4.52
1506 1517 2.463757 TACGAACGTTTTTCGCGGCG 62.464 55.000 17.70 17.70 44.98 6.46
1514 1525 6.402875 GGAAGGATAGCATTTACGAACGTTTT 60.403 38.462 0.46 0.00 0.00 2.43
1656 1668 1.792006 AGGTAGAAAAACACGCGAGG 58.208 50.000 15.93 7.12 0.00 4.63
1696 1708 2.794103 AGTGTTGACCTTGCATGCATA 58.206 42.857 23.37 11.55 0.00 3.14
1800 1824 2.624838 CTGCCAAGAAATGTTGACCACT 59.375 45.455 0.00 0.00 0.00 4.00
1801 1825 2.622942 TCTGCCAAGAAATGTTGACCAC 59.377 45.455 0.00 0.00 0.00 4.16
1802 1826 2.622942 GTCTGCCAAGAAATGTTGACCA 59.377 45.455 0.00 0.00 33.05 4.02
1803 1827 2.350772 CGTCTGCCAAGAAATGTTGACC 60.351 50.000 0.00 0.00 33.05 4.02
1804 1828 2.350772 CCGTCTGCCAAGAAATGTTGAC 60.351 50.000 0.00 0.00 33.05 3.18
1805 1829 1.879380 CCGTCTGCCAAGAAATGTTGA 59.121 47.619 0.00 0.00 33.05 3.18
1806 1830 1.068333 CCCGTCTGCCAAGAAATGTTG 60.068 52.381 0.00 0.00 33.05 3.33
1807 1831 1.202879 TCCCGTCTGCCAAGAAATGTT 60.203 47.619 0.00 0.00 33.05 2.71
1808 1832 0.400213 TCCCGTCTGCCAAGAAATGT 59.600 50.000 0.00 0.00 33.05 2.71
1809 1833 0.804989 GTCCCGTCTGCCAAGAAATG 59.195 55.000 0.00 0.00 33.05 2.32
1810 1834 0.400213 TGTCCCGTCTGCCAAGAAAT 59.600 50.000 0.00 0.00 33.05 2.17
1811 1835 0.181587 TTGTCCCGTCTGCCAAGAAA 59.818 50.000 0.00 0.00 33.05 2.52
1822 1846 1.172180 CCACATGCAACTTGTCCCGT 61.172 55.000 0.00 0.00 0.00 5.28
1833 1857 1.889573 TTCGTTCACGCCACATGCA 60.890 52.632 0.00 0.00 41.33 3.96
1834 1858 1.440353 GTTCGTTCACGCCACATGC 60.440 57.895 0.00 0.00 39.60 4.06
1835 1859 0.110688 CAGTTCGTTCACGCCACATG 60.111 55.000 0.00 0.00 39.60 3.21
1836 1860 0.531974 ACAGTTCGTTCACGCCACAT 60.532 50.000 0.00 0.00 39.60 3.21
1857 1881 4.896482 ACTTCTTCTCACTCTGTAAGGTGT 59.104 41.667 0.00 0.00 36.76 4.16
1859 1883 4.282195 CCACTTCTTCTCACTCTGTAAGGT 59.718 45.833 0.00 0.00 0.00 3.50
1860 1884 4.815269 CCACTTCTTCTCACTCTGTAAGG 58.185 47.826 0.00 0.00 0.00 2.69
1861 1885 4.241681 GCCACTTCTTCTCACTCTGTAAG 58.758 47.826 0.00 0.00 0.00 2.34
1862 1886 3.305403 CGCCACTTCTTCTCACTCTGTAA 60.305 47.826 0.00 0.00 0.00 2.41
1863 1887 2.229062 CGCCACTTCTTCTCACTCTGTA 59.771 50.000 0.00 0.00 0.00 2.74
1864 1888 1.000283 CGCCACTTCTTCTCACTCTGT 60.000 52.381 0.00 0.00 0.00 3.41
1918 1942 1.943116 TTCTCTCTCCTGCGAGCTGC 61.943 60.000 0.00 0.00 46.70 5.25
1919 1943 0.101040 CTTCTCTCTCCTGCGAGCTG 59.899 60.000 0.00 0.00 35.94 4.24
1920 1944 1.037030 CCTTCTCTCTCCTGCGAGCT 61.037 60.000 0.00 0.00 35.94 4.09
1921 1945 1.319614 ACCTTCTCTCTCCTGCGAGC 61.320 60.000 0.00 0.00 35.94 5.03
1922 1946 0.455410 CACCTTCTCTCTCCTGCGAG 59.545 60.000 0.00 0.00 37.48 5.03
1923 1947 0.967887 CCACCTTCTCTCTCCTGCGA 60.968 60.000 0.00 0.00 0.00 5.10
1924 1948 1.515020 CCACCTTCTCTCTCCTGCG 59.485 63.158 0.00 0.00 0.00 5.18
1925 1949 1.220477 GCCACCTTCTCTCTCCTGC 59.780 63.158 0.00 0.00 0.00 4.85
1926 1950 1.904032 GGCCACCTTCTCTCTCCTG 59.096 63.158 0.00 0.00 0.00 3.86
1927 1951 1.684049 CGGCCACCTTCTCTCTCCT 60.684 63.158 2.24 0.00 0.00 3.69
2042 2066 2.191513 CAAGCAGCACAGTGGCACT 61.192 57.895 15.88 15.88 35.83 4.40
2132 2160 5.861251 TGAATTTCGATATGCACCAACAAAC 59.139 36.000 0.00 0.00 0.00 2.93
2144 2172 4.780815 TCCAAGTGGCTGAATTTCGATAT 58.219 39.130 0.00 0.00 34.44 1.63
2202 2236 3.303938 TGGCAGATGGAAGAAACCAAAA 58.696 40.909 0.00 0.00 43.47 2.44
2203 2237 2.892852 CTGGCAGATGGAAGAAACCAAA 59.107 45.455 9.42 0.00 43.47 3.28
2204 2238 2.108075 TCTGGCAGATGGAAGAAACCAA 59.892 45.455 14.43 0.00 43.47 3.67
2205 2239 1.704628 TCTGGCAGATGGAAGAAACCA 59.295 47.619 14.43 0.00 44.41 3.67
2206 2240 2.496899 TCTGGCAGATGGAAGAAACC 57.503 50.000 14.43 0.00 0.00 3.27
2231 2433 1.300481 GGCTAACCGATGAAGAAGCC 58.700 55.000 0.00 0.00 42.40 4.35
2244 2446 1.519498 ACATAGGGGAAGGGGCTAAC 58.481 55.000 0.00 0.00 0.00 2.34
2249 2451 2.919772 AAACAACATAGGGGAAGGGG 57.080 50.000 0.00 0.00 0.00 4.79
2317 2523 9.541143 AAACACCAAAGATTTGACGATAAAAAT 57.459 25.926 6.87 0.00 40.55 1.82
2327 2533 7.035004 CACAAAGAGAAACACCAAAGATTTGA 58.965 34.615 6.87 0.00 40.55 2.69
2372 2580 4.524749 CGAAATTCAGCTCGATCGTAGTA 58.475 43.478 15.94 0.00 37.23 1.82
2386 2594 1.453155 GAGGAAGCTGGCGAAATTCA 58.547 50.000 0.00 0.00 0.00 2.57
2416 2653 1.338200 CCCGGAATAGGCATAGACAGC 60.338 57.143 0.73 0.00 0.00 4.40
2417 2654 2.028930 GTCCCGGAATAGGCATAGACAG 60.029 54.545 0.73 0.00 0.00 3.51
2418 2655 1.968493 GTCCCGGAATAGGCATAGACA 59.032 52.381 0.73 0.00 0.00 3.41
2419 2656 1.968493 TGTCCCGGAATAGGCATAGAC 59.032 52.381 0.73 0.00 0.00 2.59
2420 2657 2.391926 TGTCCCGGAATAGGCATAGA 57.608 50.000 0.73 0.00 0.00 1.98
2421 2658 3.485463 TTTGTCCCGGAATAGGCATAG 57.515 47.619 0.73 0.00 0.00 2.23
2422 2659 3.497763 CCATTTGTCCCGGAATAGGCATA 60.498 47.826 0.73 0.00 0.00 3.14
2423 2660 2.586425 CATTTGTCCCGGAATAGGCAT 58.414 47.619 0.73 0.00 0.00 4.40
2424 2661 1.409521 CCATTTGTCCCGGAATAGGCA 60.410 52.381 0.73 0.00 0.00 4.75
2425 2662 1.133915 TCCATTTGTCCCGGAATAGGC 60.134 52.381 0.73 0.00 0.00 3.93
2426 2663 2.487265 CCTCCATTTGTCCCGGAATAGG 60.487 54.545 0.73 0.00 0.00 2.57
2427 2664 2.851195 CCTCCATTTGTCCCGGAATAG 58.149 52.381 0.73 0.00 0.00 1.73
2428 2665 1.133915 GCCTCCATTTGTCCCGGAATA 60.134 52.381 0.73 0.00 0.00 1.75
2429 2666 0.395724 GCCTCCATTTGTCCCGGAAT 60.396 55.000 0.73 0.00 0.00 3.01
2430 2667 1.001393 GCCTCCATTTGTCCCGGAA 60.001 57.895 0.73 0.00 0.00 4.30
2431 2668 2.674754 GCCTCCATTTGTCCCGGA 59.325 61.111 0.73 0.00 0.00 5.14
2432 2669 2.824041 CGCCTCCATTTGTCCCGG 60.824 66.667 0.00 0.00 0.00 5.73
2433 2670 3.508840 GCGCCTCCATTTGTCCCG 61.509 66.667 0.00 0.00 0.00 5.14
2434 2671 1.937546 CTTGCGCCTCCATTTGTCCC 61.938 60.000 4.18 0.00 0.00 4.46
2435 2672 0.960364 TCTTGCGCCTCCATTTGTCC 60.960 55.000 4.18 0.00 0.00 4.02
2436 2673 0.449388 CTCTTGCGCCTCCATTTGTC 59.551 55.000 4.18 0.00 0.00 3.18
2437 2674 0.036732 TCTCTTGCGCCTCCATTTGT 59.963 50.000 4.18 0.00 0.00 2.83
2438 2675 0.449388 GTCTCTTGCGCCTCCATTTG 59.551 55.000 4.18 0.00 0.00 2.32
2439 2676 1.021390 CGTCTCTTGCGCCTCCATTT 61.021 55.000 4.18 0.00 0.00 2.32
2440 2677 1.448540 CGTCTCTTGCGCCTCCATT 60.449 57.895 4.18 0.00 0.00 3.16
2441 2678 2.185350 CGTCTCTTGCGCCTCCAT 59.815 61.111 4.18 0.00 0.00 3.41
2885 3134 8.733458 CACTTGAATTCTTCAGTGATGGAATTA 58.267 33.333 22.98 14.06 41.38 1.40
2898 3147 3.926616 TCCGGAGACACTTGAATTCTTC 58.073 45.455 0.00 0.00 0.00 2.87
2909 3158 3.490800 GAGTCTAAACTCCGGAGACAC 57.509 52.381 37.69 22.61 45.26 3.67
2922 3171 4.416516 TCAGATCAGGTGTTGGAGTCTAA 58.583 43.478 0.00 0.00 0.00 2.10
2924 3173 2.894731 TCAGATCAGGTGTTGGAGTCT 58.105 47.619 0.00 0.00 0.00 3.24
2929 3178 2.238144 AGGTGATCAGATCAGGTGTTGG 59.762 50.000 13.78 0.00 40.53 3.77
2932 3181 1.836166 CCAGGTGATCAGATCAGGTGT 59.164 52.381 13.78 0.00 40.53 4.16
2935 3200 1.070445 GAGCCAGGTGATCAGATCAGG 59.930 57.143 13.78 12.38 40.53 3.86
2947 3212 2.370718 CTGAACAGGAGAGCCAGGT 58.629 57.895 0.00 0.00 36.29 4.00
2986 3251 0.756294 TGCCGAGAAACTGAACCTCA 59.244 50.000 0.00 0.00 0.00 3.86
2992 3257 0.389817 CCACGATGCCGAGAAACTGA 60.390 55.000 0.00 0.00 39.50 3.41
2995 3260 1.696832 GCTCCACGATGCCGAGAAAC 61.697 60.000 0.00 0.00 39.50 2.78
2998 3263 3.068064 TGCTCCACGATGCCGAGA 61.068 61.111 0.00 0.00 39.50 4.04
3010 3275 3.644399 GACGAGGTTCGGGTGCTCC 62.644 68.421 3.37 0.00 45.59 4.70
3148 3413 1.676968 CAACCTGACGTCCCATGGA 59.323 57.895 15.22 0.00 0.00 3.41
3208 3473 1.681666 CTGAAGCTCAAGGCCCTCA 59.318 57.895 0.00 0.00 43.05 3.86
3345 3618 2.418692 CATGATCTGATGAGAGCTGCC 58.581 52.381 0.00 0.00 35.50 4.85
3386 3659 6.864342 TCTGACTTTTCCATGTAGTACTAGC 58.136 40.000 1.87 0.00 0.00 3.42
3388 3661 8.812972 ACATTCTGACTTTTCCATGTAGTACTA 58.187 33.333 0.00 0.00 0.00 1.82
3389 3662 7.680730 ACATTCTGACTTTTCCATGTAGTACT 58.319 34.615 0.00 0.00 0.00 2.73
3390 3663 7.907214 ACATTCTGACTTTTCCATGTAGTAC 57.093 36.000 0.00 0.00 0.00 2.73
3395 3668 6.713762 TTGAACATTCTGACTTTTCCATGT 57.286 33.333 0.00 0.00 0.00 3.21
3406 3679 7.201758 GGCTGTGATGATAATTGAACATTCTGA 60.202 37.037 0.00 0.00 0.00 3.27
3411 3684 6.124340 TCAGGCTGTGATGATAATTGAACAT 58.876 36.000 15.27 0.00 0.00 2.71
3486 3765 3.829948 CAGTATGTTTGCAGCCTTGAAG 58.170 45.455 0.00 0.00 0.00 3.02
3528 3807 2.833631 ATCCGAAGTCCGACAGTTTT 57.166 45.000 0.40 0.00 41.76 2.43
3534 3813 2.194271 CTTGCTAATCCGAAGTCCGAC 58.806 52.381 0.00 0.00 41.76 4.79
3543 3822 1.451936 CCCCTCCCTTGCTAATCCG 59.548 63.158 0.00 0.00 0.00 4.18
3567 3846 2.443255 AGACACATGGGTTTGACCTTCT 59.557 45.455 0.00 0.00 38.64 2.85
3585 3864 7.387948 AGTGAAATTTGACATACCACTGTAGAC 59.612 37.037 10.48 0.00 32.85 2.59
3605 3885 5.664294 TTGAGCCGGTTACTATAGTGAAA 57.336 39.130 15.90 0.00 0.00 2.69
3613 3893 4.258543 CAAGGAAATTGAGCCGGTTACTA 58.741 43.478 1.90 0.00 41.83 1.82
3698 3980 4.866486 CCATTACCTGAATTTGCAAAGAGC 59.134 41.667 18.19 9.54 45.96 4.09
3699 3981 5.185635 TCCCATTACCTGAATTTGCAAAGAG 59.814 40.000 18.19 12.37 0.00 2.85
3700 3982 5.083122 TCCCATTACCTGAATTTGCAAAGA 58.917 37.500 18.19 3.26 0.00 2.52
3759 4052 1.379044 CTTGGTGGTGAGATGCCCC 60.379 63.158 0.00 0.00 0.00 5.80
4083 4376 0.458543 CCTCCACTGAACGGACATCG 60.459 60.000 0.00 0.00 45.88 3.84
4109 4402 0.401356 TGGTGCCTCATGAAGAAGCA 59.599 50.000 0.00 0.00 41.27 3.91
4140 4433 1.475169 CCGCAGCCTCATCCTCCATA 61.475 60.000 0.00 0.00 0.00 2.74
4273 4567 4.378770 GCAAAATCAAGAGCTCAACGATGA 60.379 41.667 17.77 11.88 0.00 2.92
4296 4590 5.810074 AGAACAACAAGAAAACAAAATCCGG 59.190 36.000 0.00 0.00 0.00 5.14
4368 4668 1.671979 TCAATCAGCAGCTATGGCAC 58.328 50.000 3.10 0.00 41.70 5.01
4380 4680 7.533426 CCCTTCAAACTTTACTCATCAATCAG 58.467 38.462 0.00 0.00 0.00 2.90
4404 4704 2.291996 ACCTATTTTTACCACCCCAGCC 60.292 50.000 0.00 0.00 0.00 4.85
4486 4789 8.766994 AATAGTAGGCACCATTTTCATGTATT 57.233 30.769 0.00 0.00 0.00 1.89
4538 4841 8.628882 AATAAAATAAAATAGCGTGCTTCCAC 57.371 30.769 0.00 0.00 38.62 4.02
4643 4951 7.171630 TCCTCCTGTAGTTAGAAATTCACTC 57.828 40.000 0.00 0.00 0.00 3.51
4650 4958 6.312529 TCTCTGTTCCTCCTGTAGTTAGAAA 58.687 40.000 0.00 0.00 0.00 2.52
4651 4959 5.888901 TCTCTGTTCCTCCTGTAGTTAGAA 58.111 41.667 0.00 0.00 0.00 2.10
4703 5011 1.028868 CCTGGCCTTTACAGCTCAGC 61.029 60.000 3.32 0.00 34.65 4.26
4804 5112 7.724506 TGAGGGTATAATAGACTAGTCACAAGG 59.275 40.741 24.44 0.00 0.00 3.61
4808 5116 8.569641 CAGTTGAGGGTATAATAGACTAGTCAC 58.430 40.741 24.44 12.26 0.00 3.67
4945 5291 1.134491 TGCTGATGCTGACTGAGATGG 60.134 52.381 0.00 0.00 40.48 3.51
4999 5345 5.767665 TCTGTTGTTACAATGCCACACTTAT 59.232 36.000 0.00 0.00 32.92 1.73
5032 5378 6.804783 ACACTGTTGTTTAAGAAAAAGAACCG 59.195 34.615 7.70 4.82 28.43 4.44
5087 5433 4.865776 TGCTGGTTTTTAATTCTTCGGTG 58.134 39.130 0.00 0.00 0.00 4.94
5088 5434 4.825085 TCTGCTGGTTTTTAATTCTTCGGT 59.175 37.500 0.00 0.00 0.00 4.69
5106 5452 0.982704 ACTCATGACCTGCTTCTGCT 59.017 50.000 0.00 0.00 40.48 4.24
5136 5482 3.726557 TTCCCATTGCTGAGAACTGAT 57.273 42.857 0.00 0.00 0.00 2.90
5188 5534 1.000506 ACCGTGAACGTCAAGTGCTAT 59.999 47.619 1.75 0.00 37.74 2.97
5206 5552 1.080974 CGATATCGGCCCGTACACC 60.081 63.158 17.51 0.00 35.37 4.16
5242 5588 3.181445 ACACACTGTGCTTCTTTATGGGA 60.181 43.478 9.20 0.00 36.98 4.37


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.